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Unknown,Transcriptomics,Genomics,Proteomics

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Gene-regulatory networks activated by pattern-specific generation of action potentials in dorsal root ganglia neurons

ABSTRACT: Development and plasticity in the nervous system are regulated by specific patterns of neural impulse activity. Patterned activity orchestrates spatial and temporal changes in the expression of networks of genes. These gene regulatory networks underlie the long-term changes in cell specification, growth of synaptic connections, and frequency adaptation that occur throughout neonatal and postnatal life. We show that the temporal nature of action potentials and downstream signaling differentially regulate the expression of hundreds of diverse neuronal genes through distinct gene regulatory networks. Analysis of upstream regulatory regions showed enrichment in transcription factor binding sites for NF-Kappa that was action potential firing pattern specific. Our new findings demonstrate spike-frequency decoding by action potentials at the transcriptional level by pattern-specific activation of transcription factors and associated gene-regulatory networks that operate to adjust the modalities of sensory neurons. We analyzed the transcriptomic changes in primary cultures of embronic dorsal root ganglia (DRG) neurons subjected to four electric stimulation patterns with respect to their non-stimulated counterparts. We have adopted the multiple yellow strategy in which differently fluorescent labeled biological replicas are co-hybridized with each array and then similarly labeled samples from cells subjected to different conditions are compared and results averaged over the two labels.

ORGANISM(S): Mus musculus

SUBMITTER: Dumitru Iacobas

PROVIDER: E-GEOD-84872 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene-regulatory networks activated by pattern-specific generation of action potentials in dorsal root ganglia neurons

Project description:Development and plasticity in the nervous system are regulated by specific patterns of neural impulse activity. Patterned activity orchestrates spatial and temporal changes in the expression of networks of genes. These gene regulatory networks underlie the long-term changes in cell specification, growth of synaptic connections, and frequency adaptation that occur throughout neonatal and postnatal life. We show that the temporal nature of action potentials and downstream signaling differentially regulate the expression of hundreds of diverse neuronal genes through distinct gene regulatory networks. Analysis of upstream regulatory regions showed enrichment in transcription factor binding sites for NF-Kappa that was action potential firing pattern specific. Our new findings demonstrate spike-frequency decoding by action potentials at the transcriptional level by pattern-specific activation of transcription factors and associated gene-regulatory networks that operate to adjust the modalities of sensory neurons.

2016-07-26 | GSE84872 | GEO

Transcriptomic effects of prenatal exposure to corticosteroids on synaptic transmission

Project description:Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the prefrontal cortex of female rats prenatally exposed to either betamethasone or saline. The transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. We analyzed how composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission) are afected by the prenatal exposure to corticosteroids and postnatal ketamine-induced seizures. One sex (F) x two prenatal exposures (B = betamethasone, S = saline) x two postnatal treatments (K = ketamine, S = saline). Biological replicates: 4 FSS, 4 FBS, 4 FBK.

2016-01-09 | E-GEOD-76694 | biostudies-arrayexpress

Transcriptomic effects of early life and peripubertal dietary vitamin D deficiency on mouse ovaries

Project description:Vitamin D2 (VD) and the VD3 receptor (VDR) are proposed to have multiple important physiological roles that include but are not limited to glucose homeostasis, bone health, immune competency and more recently maintenance of normal reproductive physiology. The prevalence of VD deficiency in the US is reported to be as high as 60% in some populations. Several recent studies suggest that reproductive-aged women and their offspring are at the greatest risk for VD deficiency. The objective of our study was to determine the effect of early life (intrauterine through preweaning) and peripubertal VD deficiency on female reproductive physiology. Profile and compare the ovarian transcriptomes of 2-month-old C57BL/6J mice that received a normal (OC samples) or a VD-deficient diet only during the early life (OE samples) or peripubertal (OP samples). Each diet group (OC, OE and OP) was composed of 4 females (biological replicas).

2013-06-21 | E-GEOD-48167 | biostudies-arrayexpress

Transcriptomic effects of early life and peripubertal dietary vitamin D deficiency on mouse pituitary gland

Project description:Vitamin D2 (VD) and the VD3 receptor (VDR) are proposed to have multiple important physiological roles that include but are not limited to glucose homeostasis, bone health, immune competency and more recently maintenance of normal reproductive physiology. The prevalence of VD deficiency in the US is reported to be as high as 60% in some populations. Several recent studies suggest that reproductive-aged women and their offspring are at the greatest risk for VD deficiency. The objective of our study was to determine the effect of early life (intrauterine through preweaning) and peripubertal VD deficiency on female reproductive physiology. Profile and compare the hypophysis transcriptomes of 2-month-old C57BL/6J mice that received a normal (OC samples) or a VD-deficient diet only during the early life (OE samples) or peripubertal (OP samples). Each diet group (OC, OE and OP) was composed of 4 females (biological replicas).

2013-06-21 | E-GEOD-48169 | biostudies-arrayexpress

Transcriptomic effects of early life and peripubertal dietary vitamin D deficiency on mouse ovaries and pituitary glands

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-06-21 | E-GEOD-48170 | biostudies-arrayexpress

Left-right transcriptomic differences in adult male mouse heart atria

Project description:Left and right heart atria of adult male mice were profiled to determine the differences in gene expression, control, coordination and signaling fabrics Two-sides (L= left, R = right) gene expression profiling experiment in adult mouse male (M) atria (A). 4 biological replicates: MAL1-4, MAR1-4. This experiment used our standard multiple yellow strategy in which Cy3 and Cy5 labeled biological replicates are cohybridized with a two-color array and each channel is processed independently.

2013-03-20 | E-GEOD-45339 | biostudies-arrayexpress

Left-right transcriptomic differences in adult male mouse heart ventricles

Project description:Left and right heart ventricles of adult male mice were profiled to determine the differences in gene expression, control, coordination and signaling fabrics Two-sides (L= left, R = right) gene expression profiling experiment in adult mouse male (M) ventricles (V). 4 biological replicates: MVL1-4, MVR1-4.

2013-03-21 | E-GEOD-45348 | biostudies-arrayexpress

Remodeling of major genomic fabrics and their interplay in metastatic clear cell renal carcinoma

Project description:Clear cell renal carcinoma (CCRC) accounts for >80% of all kidney cancers but what triggers the tumorigenesis in the kidney and metastases in the bones are still under debate. Our hypothesis is that remodeling of the genomic fabrics of certain functional pathways and their interplay beyond critical limits are key causes of CCRC. We profiled the transcriptomes of metastatic chest wall and of two primary cancerous sites of the renal medulla and compared them with that of non-cancerous kidney resection margins. Samples were collected from a 74 years old male with metastatic carcinoma, consistent with renal cell carcinoma, clear cell type, Fuhrman grade 3, who undergone total right kidney nephrectomy and resection of a chest wall mass. Transcriptomic analysis pointed the tumor region in the right kidney that led to the chest wall metastases. The tumor proved heterogeneous not only in the expression level but also in the expression control, coordination and interplay of pathways responsible for cellular processes and genetic and environmental information processing. The differently regulated pathways in the two sides of the tumor: CCRC, and HIF-1, Vegfa and mTor signaling indicate activation of distinct mechanisms. Four-conditions (CTR = control - non-cancerous kidney resection margins, PTA = primary tumor side A, PTB = primary tumor side B, MET = chest wall metastasis. Four biological replicates of each condition.

2015-08-24 | E-GEOD-72304 | biostudies-arrayexpress

Remodeling of DNA transcription genomic fabric in Capridine-treated LNCaP human prostate cancer cell line

Project description:Capridine is a chemotherapeutic agent with specificity towards prostate cancer and minimal bone marrow toxicity. Capridine structure is consistent with a classical DNA intercalating agent, although its DNA intercalation property does not fully correlate with its anti prostate cancer specific activity. We have used Agilent human gene expression arrays to identify the cellular targets of Capridine on androgen responsive LNCaP cells, a classical cell lines for prostate cancer studies. We found that expression of 142 unigenes genes was altered by Capridine. Interestingly, the most altered category was that of transcription regulators: 10 down and 16 upregulated. Our data confirm that, in addition to DNA intercalation, Capridine targets DNA transcription via histone modulation in a cell-specific manner. Two-conditions: LO = not treated, LA = Capridine-treated DU145 cells. Four biological replicates of each condition. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: LO1 & LO3 were compared with LA1 & LA3, LO2 & LO4 were compared with LA2 & + LA4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

2015-08-27 | E-GEOD-72414 | biostudies-arrayexpress

Transcriptomic effects of Capridine on the acute promyelocytic leukemia HL-60 cell line

Project description:We used Agilent human gene expression arrays to test whether Capridine, a chemotherapeutic agent with specificity towards prostate cancer, deregulates the genomic fabric of acute myeloyd leukemia in HL-60 cells. This cell line was derived at the National Cancer Institute from a 36-year-old woman with acute promyelocytic leukemia. We found that Capridine down-regulates the pathways responsible for formation of hematopoietic progenitor cells, for anti-apoptosis and for proliferation of clonal neoplastic cells. Our results indicates the therapeutic potential of Capridine against acute myeloid leukemia. Two-conditions: HO = not treated, HA = Capridine-treated HL-60 cells. Four biological replicates of each condition. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: HO1 & HO3 were compared with HA1 & HA3, HO2 & HO4 were compared with HA2 & + HA4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

2015-08-27 | E-GEOD-72415 | biostudies-arrayexpress

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